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porous media  Department of Environmental Sciences   Riverside, CA, US porous media  Department of Environmental Sciences   Riverside, CA, US

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porous media Department of Environmental Sciences Riverside, CA, US - PPT Presentation

CEN Belgium EPORT OF THE Notes on HP1 ID: 453090

CEN Belgium EPORT THE Notes

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CEN porous media Department of Environmental Sciences Riverside, CA, USA Jiri.Simunek@ucr.edu Belgium EPORT OF THE Notes on HP1 – a software package for simulating variably-saturated water flow, heat transport, solute transport, and biogeochemistry in porous media Department of Environmental Sciences Riverside, CA, USA Jiri.Simunek@ucr.edu Belgium 1 Introduction.............................................................................................................................1 2 Running HP1 from the HYDRUS-1D Graphical User Interface............................................2 2.1 Differences Between Version 2.2.002 of Versions of HP1 and HYDRUS-1D............................................................................................2 2.2 Manage HP1 Projects......................................................................................................3 2.3 Create a New Project.......................................................................................................2.4 Define the Physical Part of a Project...............................................................................3 2.5 Define the Thermodynamic Database.............................................................................4 2.6 Define Components.........................................................................................................42.7 Create the phreeqc.in File................................................................................................52.7.1 Options to create and modify the phreeqc.in file....................................................5 2.7.2 Structured phreeqc.in File.......................................................................................6 2.7.3 Modify the Structured phreeqc.in File....................................................................8 2.7.4 Define Additions to the Thermodynamic Database................................................8 2.7.5 Define the Composition of Initial and Boundary Solutions....................................9 2.7.6 Define the Geochemical Model...............................................................................9 2.7.7 Define the Output..................................................................................................10 2.8 Define the Spatial Distribution of the InitiaBoundary Solutions...................................................................................................................10 2.9 Control Output...............................................................................................................11 2.9.1 Punch Times and Locations..................................................................................11 2.9.2 Selected Output.....................................................................................................13 2.9.3 Print Options.........................................................................................................13 2.9.4 PHREEQC Dump..................................................................................................13 2.9.5 HP1 Output Files with Geochemical Information.................................................13 2.10 Create Templates to Produce Graphs with GNUPLOT................................................15 2.11 Running a HP1 Project..................................................................................................16 2.12 Looking at Selected Numerical Results........................................................................16 2.13 Help File........................................................................................................................16 3 Examples Installed with HP1................................................................................................183.1 EqCl: Physical Equilibrium Transport of Cl for Steady-State Flow Conditions..........18 3.2 NEQCL: Physical Nonequilibrium Transport of Cl for Steady-State Flow Conditions18 3.3 TRANSCL: Physical NonequiConditions.................................................................................................................................19 3.4 STADS: Transport of nonlinearly adsorbed contaminant for steady-state flow conditions..................................................................................................................................20 3.5 STDECAY: Transport of Nonlinearly Adsorbing Contaminant with First-Order Decay for Steady-State Flow Conditions.............................................................................................213.6 SEASONCHAIN: First-Order Decay Chain of Nonlinearly Adsorbing Contaminants During Unsteady Flow..............................................................................................................22 3.7 CATEXCH: Transport of Heavy Metals Subject to Multiple Cation Exchange..........23 3.8 MINDIS: Transport with Mineral Dissolution..............................................................27 3.9 MCATEXCH: Transport of Heavy Metals in a Porous Medium with a pH-Dependent Cation Exchange Complex........................................................................................................4 Step-By-Step Instructions for Selected Examples................................................................32 4.1 Dissolution of Gypsum and Calcite..............................................................................32 4.1.1 Problem Definition................................................................................................32 4.1.2 Input......................................................................................................................32 4.1.3 Output....................................................................................................................35 4.12.2 Problem Definition................................................................................................92 4.12.3 Input......................................................................................................................93 4.12.4 Output....................................................................................................................96 References.............................................................................................................................98 r simulating variably-saturated and biogeochemistry in porous media. Version 2.2. SCK•CEN, Mol, Belgium, BLG-1068. HP1 is a comprehensive modeling tool in terms of processes and reactions for simulating reactive transport and biogeochemical processes in variably-saturated porous media. HP1 results from coupling the water and solute transport model HYDRUS-1D (Šimnek et al., 2009a) and PHREEQC-2 (Parkhurst and Appelo, 1999). This note provides an overview of how to set up and execute a HP1 project using version 2.2.002 of HP1 and version 4.13 of the graphical user interface (GUI) of HYDRUS-1D. Version 2.2 of HP1 is embedded in the graphical interface of version 4.13 of HYDRUS-1D. The graphical user interface of HYDRUS-1D (H1D GUI) provides support to the HP1 code in order (water flow, solute tranDefine the thermodynamic database Define the components foCreate the phreeqc.in input file Define additions to the thermodynamic database Define the composition of the initial and boundary solutions Define the geochemical model Define the spatial distribution of the initial solutions and the temporal variation of the Create templates to produce graphs with GNUPLOT Run HP1 projects Display selected numerical results Display the help file A large part of this note are step-by-step instructions for selected examples involving mineral dissolution and precipitation, cation exchange, surface complexation and kinetic degradation networks. The implementation of variably-saturated flow conditions, changing boundary KeywordsHP1, reactive transport model, variably-saturated water flow, multicomponent solute transport, heat transport, biogeochemical processes, numerical model, HYDRUS-1D Table 1 Hydrological, transport, and reaction parameters for the example SEASONCHAIN...............................22Table 2 Initial and inflow concentrations for the example CATEXCH...................................................................24Table 3 pH and solution concentrations used in the simulation (µmol l............................................................29Table 4 Soil hydraulic properties and cation exchange capacities of five soil layers (Seuntjens, 2000)................29Table 5 Overview of aqueous equilibrium reactions and corresponding equilibrium constants (data from phreeqc.dat database, Parkhurst and Appelo, 1999).......................................................................................29Table 6 Log K parameters for multi-site exchange complex....................................................................................30Table 7 Soil hydraulic and other properties of six soil horizons (from Seuntjens, 2000).......................................55Table 8 Initial pH and concentration for 9 components..........................................................................................55Table 9 Definition of parameters and their values for the PCE biodegradation problem (from Case 1 and 2 in Sun et al., 2004). Rate parameters are for a reference temperature of 20°C.................................................78 Figure 1 - Time series of Cl at two depths for the example EQCL. 18Figure 2 - Time series of Cl at two depths for the example NEQCL. 19Figure 3 – Time series of Cl concentrations in the mobile phase at four depths for the example TRANSCL. 20Figure 4 – Profile plots of Cl concentrations in the mobile phase (left) and immobile phase (right) at selected times for the example TRANSCL. 20Figure 5 – Profiles of Pola concentrations for the example STADS. 21Figure 6 – Profiles of Pola concentrations for the example STDECAY. 21Figure 7 – Profile plots of Conta, Contb and Contc concentrations at selected times for the example SEASONCHAIN. Figure 8 – Time series of pH (top left), total concentrations of Ca (top right), Cd (bottom left), and Zn (bottom right) at four depths for the example CATEXCH. 24Figure 9 – Time series of molalities of sorbed K (top left), Ca (top right), Cd (bottom left), and Zn (bottom right) at four depths for the example CATEXCH. 25Figure 10 – Profiles of pH (top left), Ca (top right), Cd (bottom left), and Zn (bottom right) at selected times for the example CATEXCH. 26Figure 11 – Profiles of molalities of sorbed K (top left), Ca (top right), Cd (bottom left), and Zn (bottom right) at selected times for the example CATEXCH. 27Figure 12 – Profiles of pH (top), total Si (middle left) and Al (middle right) concentrations, and amounts of amorf SiO (bottom left) and gibbsite (bottom right) at selected times for the example MINDIS. 28Figure 13 – Outflow curves of pH (left) and Cd (right) for the example MCATEXCH. 30Figure 14 – Profiles of pH (top left), Cd (top right), the fraction of deprotonated cation exchange sites (bottom left), and the fraction of cation exchange sites with Cd (bottom right) at selected times for the example MCATEXCH. Figure 15 – Profiles of pH (top left), total aqueous C concentration (top right), total aqueous Ca concentration (middle left), total aqueous S concentration (middle right), the amount of gypsum (bottom left), and the amount of calcite (bottom right) at selected print times during dissolution of calcite and gypsum. 38Figure 16 – Time series of pH (top left), total aqueous C concentration (top right), total aqueous Ca concentration (middle left), total aqueous S con the amount of gypsum (bottom left), and the amount of calcite (bottom right) at selected depths (observation nodes) during dissolution of calcite and gypsum. 39Figure 17 – Profiles of total aqueous Cd (top left), the amount of otavite (top right), and the percentage of Cd in solution (bottom) at selected print times during dissolution of calcite and gypsum and Cd transport.Figure 18 – Comparison between a simulation when a solution with a low Cl concentration enters the system (described in paragraph 4.2, left figures) and a simulation when a solution with a high Cl concentration enters the system after 1 day (described in paragraph 4.3, right figures) for time series of Cd concentrations at different depths (top figures) and profiles of the amount of otavite (bottom figures). 44Figure 19 – Time series of Cl at selected depths (observation nodes) for the example described in section 4.3.Figure 20 – Outflow concentrations of Cl, Ca, Na, and K for the single-pulse cation exchange example. 50Figure 21 – Time series of K concentrations at four depths for the multiple-pulse cation exchange example. 53Figure 22 – Outflow concentrations for the multiple-pulse cation exchange example. 54Figure 23 – Time series of Cl (top left), Ca (top right), and Cd (bottom) concentrations at selected depths (observation nodes) for the example described in section 4.6. 63Figure 24 – Profiles of water content (top left), and total aqueous concentrations of Cl, Na, K, Ca and Mg at selected print times during horizontal infiltration of multiple cations (the example is described in section 4.7). Figure 25 – Profiles of sorbed concentrations of Na, K, Ca, and Mg at selected print times during horizontal infiltration of multiple cations (the example is described in section 4.7). 71Profiles of aqueous concentration of U for the example described in section 4.8. 76Figure 27 – Perchloroethylene (PCE) degradation pathway. (Figure from Schaerlaekens et al., 1999). 77 – Degradation pathway of PCE using first-order rate constants. 78Time series of Dcecis (left) and Vc (righ ) at selected depths (observation nodes) for the example described in section 4.9. Figure 30 – Profiles of Tce (left) and Eth (righ ) at selected print times for the example described in paragraph 4.9. Outflow curves for the example described in section 4.9. 84Profiles of the solid phase PCE_lq (left) and the aqueous concentrations of Pce (right) at selected print times for the example described in section 4.10. 87 Introduction HP1 is a comprehensive modeling tool in terms of processes and reactions for simulating reactive transport and biogeochemical processes in variably-saturated porous media. HP1 results from coupling the water and solute transport model HYDRUS-1D (Šimnek et al., 2009a) and PHREEQC-2 (Parkhurst and Appelo, 1999). The combined code contains modules simulating (1) transient water flow in variably-saturated media, (2) transport of multiple components, (3) mixed equilibrium/kinetic biogeochemical reactions, and (4) heat transport. HP1 is a significant expansion of the individual HYDRUS-1D and PHREEQC programs by combining, and preserving, most of the features and capabilities of the two codes into a single numerical simulator. The code uses the Richards equation for variably-saturated flow and advection-dispersion type equations for heat and solute transport. The program can also simulate a broad range of low-temperature biogeochemical reactions in water, the vadose zone and in ground water systems, including interactions with minerals, gases, exchangers, and sorption surfaces, based on thermodynamic equilibrium, kinetics, or mixed equilibrium-kinetic reactions. Various applications of HP1 were presented by Jacques and Šimnek (2005), Jacques et al. (2006, nek et al. (2006, 2009b). The first version of HP1 was released in November 2004 and is described in Jacques and nek (2005). The HP1 version 2.2.002 (released November 2009) is different with respect to following points, amongst others: includes the computational modulis based on the source code of the HYDRUS-1D computational module rewritten in considers new components Total_O, Total_H, and Charge to allow simulations of redox processes and surface complexation allows initial concentrations of components to be zero defines solution compositions usis fully integrated in the graphical user interface of version 4.13 of HYDRUS-1D. of HP1 and version 4.13 of the graphical user interface (GUI) of HYDRUS-1D. Chapter 2 describes how an HP1 project is created, modified, and executed using GUI of HYDRUS-1D. Chapter 3 shows the implementation of the verification examples from the first manual (Jacques nek, 2005) using version 2.2 of HP1. Chapter 4 describes a number of simple HP1 step instructions for their implementation using HP1. In version 4.13 of HYDRUS-1D, the user can create a HP1 project using the H1D GUI without the need to use any external programs. The GUI of version 4.13 of HYDRUS-1D allows one to create a structured file, which can be defined and/or modified using the H1D GUI (see paragraph 2.7). Note that projects created with previous versions of HP1 or HYDRUS-1D can be opened and executed with the GUI of version 4.13 of HYDRUS-1D. Furthermore, the user can still create the file in an ASCII text editor or graphical user interface of PHREEQC. Another major difference between version 2.2.002 of HP1 and its older versions is the possibility to define the composition of the initial and boundary solutions in the phreeqc.in file. However, the spatial distribution of the initial solutions and the temporal variations of the boundary solutions are defined using the H1D GUI. In previous releases of HP1, initial solutions were defined only in the file, whereas boundary solutions were defined via the H1D GUI. Version 2.2.002 of HP1 defines solutions in terms of solution composition numbers instead of concentrations. Solution composition numbers are used to define the spatial distribution of the initial solutions and the temporal variations of the boundary solutions in the H1D GUI. Concentrations of the components of a solution composition are defined in the file. Manage HP1 Projects HP1 projects are managed in the same way as HYDRUS-1D projects using the Project Manager. The Project Manager is used to manage data of existing projects, and to locate, open, delete, copy, or rename projects. Create a New Project A new HP1 project is created using the button "New" in the Project Manager. After defining a name and a description of a project, the Main Process dialog window allows users to select the HP1 model from available solute transport models: The physical part of a HP1 project (water flow, solute transport and heat transport) is defined using the H1D GUI in the same way as for HYDRUS-1D projects. Depending on the choice of selected processes, models, and options, a number of pre-processing menus will be displayed. Options to create and modify the phreeqc.in file The H1D GUI allows for three options to create the phreeqc.in file: Create the file using the H1D GUI and modify it using an ASCII text editor or cal user interface Create and modify the phreeqc.in file using an ASCII text editor or the PHREEQC graphical user interface The selection of this option is done in the and Database Pathway dialog When the option "Create PHREEQC.IN file using HYDRUS GUI" is not selected, the When the option "In Concentrations" is selected, the approach of specifying initial and boundary conditions as described in Jacques and Šimnek (2005) has to be followed. This implies that: phreeqc.ineated and modified outside the H1D GUI, the composition of the boundary solutions hathe initial conditions and their spatial distributions have to be defined in the file When the option "In Solution Compositions" is selected without the option "Create PHREEQC.IN file using HYDRUS GUI", only solution composition numbers are phreeqc.ineated and modified outside the H1D GUI the composition of the boundary solutions has to be defined in phreeqc.in using specific solution composition numbers and . The content is defined in the editor Additions to Thermodynamic Database of the dialog window. OUTPUT This block consists of two parts. The first part starts with the PHREEQC keyword SELECTED_OUTPUT, followed by the information defined in the HP1 – Print and Punch Controlsdialog window. This block is automatically updated by the HYDRUS GUI when the project is saved. The second part contains additional specifications to be written to the output files and is typically defined using the following PHREEQC data blocks: content is defined in the editor of the SOLUTIONDEFINITION This block contains the definitions of the initial solutions and boundary solutions. The latter is only read from the input file when the radio button In Solution Compositions in the Solute Transport – HP1 Components dialog window is selected. The content is defined in the editor Definitions of Solution of the Solute Transport – HP1 Definitions INITIAL This block contains definitions of the initial solutions for each node. The block starts with an keyword. For each node, both for the mobile and immobile aqueous phases, a statement is included with the following format: solution_composition where is the solution number (equal to the node number for the mobile aqueous phase and to the node number + for the immobile aqueous phase, is the number of nodes), solution_composition is the solution composition number as defined in the H1D GUI ( Profile – Summary Soil Profile – Summary is the initial water content as defined in the H1D GUI (either as the initial water content or calculated from the initial pressure head and soil retention parameters). This block is automatically updated by the H1D GUI when the project is saved. GEOCHEMICAL This block contains the definition of the geochemical model typically using the following PHREEQC data blocks: . The content is defined in of the Solute Transport – HP1 TRANSPORT This block contains the keywords with the identifiers –reset and -warnings as defined in the HP1 – Print Define the Output The user can define additional output using the editor Additional output in the dialog window by using the PHREEQC data blocks and Depending on the options selected in the HP1 – Print and Punch Control dialog window, a number of output files is created. HP1 specific output files have the same structure as the "selected output" files of PHREEQC. n of the Initial Solutions and Temporal VariationS of the Boundary Solutions The following methods are available to define thSoil Profile – Graphical Editor module. After selecting Concentration number: 1 a range of nodes can be selected and a solution composition number can be assigned for the mobile water phase. To assign a solution composition number for the immobile water � - Sorbed Concentration Concentration number: 1 Soil Profile – Summary dialog window. Solution composition numbers are defined in the column "Cnc. Comp." for the mobile water phase and in the column "Im. C. Comp." for the immobile water phase. In case of a constant boundary condition, the boundary condition is assigned in the Solute Transport – Boundary Conditions dialog window by specifying the solution composition number. Solution composition numbers 3001 and 4001 are specified in the example below: In case of time variable boundary conditions, the boundary condition is assigned in the Boundary Conditions The H1D GUI allows users to specify times and locations, for which output variables are to be HP1 Print and Punch Controls Punch Times and Locationslected by in the PHREEQC data and are to be printed. Depending on the choice of ASCII files with tab-delimited columns. the mobile water phase If "controlled by PHREEQC" is checked, the user can defined a series of punch cells (e.g., "1 2 5 25", or "1-5 25") and a punch frequency. The punch frequency indicates the number of time steps between printing of data. All data are printed in a single output file. The user specifies the name of the output file in the This submenu allows specifying a number of output variables to be written to the selected output files. Additional variables can be specified using the PHREEQC data blocks and in the editor of the dialog window. It is not needed to specify a file name in the editor Print Options This submenu allows specifying the print times and locations to write geochemical information Print locations can be linked to the HYDRUS observation points specified in the Soil Profile – module using the option "HYDRUS Observation Nodes". Alternatively, a series of node numbers can be defined. Print times can be linked to the specified print options in the dialog window. Alternatively, a print frPHREEQC Dump The dump files created by PHREEQC give a complete geochemical state for all nodes at a given time step. It is formatted as a PHREEQC input file and can thus be used to restart a HP1 calculation after failure (some adaptations may be necessary). More information is given in the PHREEQC manual. There are options to link the times when a dump file should be created to the print times defined Print OptionsHP1 Output Files with Geochemical Information Following output files are created by HP1 (in addition to the output files created by the regular routines of the HYDRUS program): EEQC. This file contains information on different calculations steps, warnings, and a full description of the geochemical the number of Newton-Raphson iterations, and the iteration at which any infeasible solution was encountered while solving the system of nonlinear equations (An infeasible solution occurs if no solution to the equality and inequality constraints can be found.). At each iteration, the identity of any species that exceeds 30 mol (an unreasonably large number) is written to the log file and noted as an "ovenoted in the log file. The phreeqc.logfile is created when the identifier –logfile is true under the PHREEQC data block Create Templates to Produce Graphs with GNUPLOT If the options "Observ. Nodes Printed to Different Files" and "Mobile and Immobile Cells in Different Files" are checked in the dialog window, the user can also check the option "Make GNUplot Tempates" in the same dialog window. HP1 creates a series of templates , two for each variable printed in the selected output files. These variables are specified in the Selected Output section of the in or the editor in the The name of the template file can consists of: These two template files are made for each variable. The file, which begins with "", contains information to produce depth profiles of a particular variable at selected times. The times are specified as the in the Print InformationThe file, which begins with "", contains information to produces time series of a particular variable at selected observation points. The observation points are defined in the Soil Profile – Graphical Editor module. The times are defined in Print OptionsPrint InformationName of the variable: pH, pe, Temperature, Total alkalinity, Ionic strength, mass cent error on electrical balance, : total aqueous concentration (-totals in : molality (-molalities in : activity (-activities in : amount of an equilibrium phase [mol/1000 cm³] (-equilibrium_phases : change in amount of an equilibrium phase [mol/1000 cm³/time] unit : saturation index of an equilibrium phase (-saturation_indices in : amount of a kinetic reactant [mol/1000 cm³] (-kinetics in : change in amount of a kinetic reactant [mol/1000 cm³/time] (-: amount of a component in a solid solution [mol/1000 cm³] (-solid_solutioins in : value of a calculated variable (-calculate_value in 1999) for a full description of the PHREEQC keywords, identifiers and BASIC statements. Not all keywords are yet documented in the he TRANSCL: Physical Nonequilibrium Transport of Chloride for Transient Flow This problem simulates the transport of chloride through a 1-m deep soil profile subject to a transient upper boundary condition given by daily values of precipitation and evaporation over a 300-d period. Physical nonequilibrium (i.e., the presence of immobile water in the soil profile) was considered in this problem. The soil hydraulic properties are typical for a loamy soil ( = 0.078 cm = 0.43 cm = 0.036 cm = 1.56, and = 24.96 cm d, from Carsel and Parish, 1988). Solute transport parameters were as follows: a dispersivity of 8 cm, an immobile water content of 0.05 cm, and a first-order exchange coefficient of 0.0125 . Precipitation and evaporation rates were typical for the Campine region in Belgium. The soil profile was discretized into 100 elements of 1 cm each. Chloride was applied during the first 53 days of the simulation with a concentration of 0.1 mmol l. Time series of Cl outflow Similar to Verification problem 2 in Jacques and Šimnek (2005). 0 0.0001 0.0002 0.0003 0.0004 0.0005 0.0006 0.0007 0.0008 0.0009 0.001 0 10 20 30 40 50 Total concentration of Cl (mol/kg water) -20.0 cm Figure 2 - Time series of Cl at two depths for the example NEQCL. STDECAY: Transport of Nonlinearly Adsorbing Contaminant with First-Order Decay for Steady-State Flow ConditionsIn this problem, saturated steady-state water flow and single-component transport of a nonlinearly adsorbing, first-order decaying contaminant (lumn of 1-m length for a period of 1000 d are considered. Transport and reactive parameters are as followed: = 1 cm d, the saturated water content = 0.5 cm cmthe dispersivity = 1 cm, the bulk density = 1.5 g cmcm³ g, the Freundlich exponent is 0.8, and the first-order decay constant is 0.02 d Initially, no contaminant is present in the soil. The contaminant concentration in the percolating water is 1 Verification problem 4 in Jacques and Šimnek (2005). Note that in the manual of HP1 version 1.0 (Jacques and Simunek, 2005), the decay coefficient was wrongly printed as 0.2 d instead of 0.02 d -80 -60 -40 -20 0 0 0.2 0.4 0.6 0.8 1 Distance (cm) 250.00 days 500.00 days 750.00 days 1000.00 days Figure 5 – Profiles of Pola concentrations for the example STADS. -100 -80 -60 -40 -20 0 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 Distance (cm) 250.00 days 500.00 days 750.00 days 1000.00 days Figure 6 – Profiles of Pola concentrations for the example STDECAY. CATEXCH: Transport of Heavy Metals SubjIn this problem, the transport of ten components (Al, Br, Ca, Cd, Cl, K, Mg, Na, Pb, and Zn) through a soil column is modeled. Initial and inflow concentrations of the ions are given in Table 2. The cation exchange capacity is equal to 0.011 mol/1000 cm³. The soil core has a length of 8 cm and is discretized into 40 cells of 0.2 cm. The flow velocity is 2 cm d and the dispersivity is 2 cm. Simulations were performed for 15 days. The maximum time step used in HP1 was 0.015 d. Selected results are present Verification problem 6 in Jacques and Šimnek (2005). -100 -80 -60 -40 -20 0 0 0.2 0.4 0.6 0.8 1 Distance (cm) 250.00 days 500.00 days 1000.00 days 1095.00 days -100 -80 -60 -40 -20 0 0 0.02 0.04 0.06 0.08 0.1 Distance (cm) 250.00 days 500.00 days 1000.00 days 1095.00 days -100 -80 -60 -40 -20 0 0 0.02 0.04 0.06 0.08 0.1 Distance (cm) 250.00 days 500.00 days 1000.00 days 1095.00 days Figure 7 – Profile plots of Conta, Contb and Contc concentrations at selected times for the example SEASONCHAIN. 25 0 0.0005 0.001 0.0015 0.002 0.0025 0 3 6 9 12 15 KX (mol/kg water) -4.0 cm -6.0 cm -8.0 cm 0 0.002 0.004 0.006 0.008 0.01 0 3 6 9 12 15 CaX2 (mol/kg water) -4.0 cm -6.0 cm -8.0 cm 0 0.0001 0.0002 0.0003 0.0004 0.0005 0 3 6 9 12 15 CdX2 (mol/kg water) -4.0 cm -6.0 cm -8.0 cm 0 0.0003 0.0006 0.0009 0.0012 0.0015 0.0018 0 3 6 9 12 15 ZnX2 (mol/kg water) -4.0 cm -6.0 cm -8.0 cm Figure 9 – Time series of molalities of sorbed K (top left), Ca (top right), Cd (bottom left), and Zn (bottom right) at four depths for the example CATEXCH. MINDIS: Transport with Mineral DissolutionA 100-cm long soil column, consisting of amorphous SiO and gibbsite (Al(OH)), is leached with a solution containing 5.10 mol l Si, 1.10 mol l Al, and 1.10 mol l Na (to obtain an inflow pH of 11.15). Initial concentrations are 1.76 10 mol l Si, 8.87 10 mol l Al, and 1 10 mol l Na, corresponding to a pH of 6.33. In each 1-cm thick cell, 0.015 mol amorphous SiOand 0.005 mol gibbsite is present. The flow velocity is 2 cm/day and the dispersivity is 1 cm. Verification problem 7 in Jacques and Šimnek (2005). -8 -7 -6 -5 -4 -3 -2 -1 0 0 0.0005 0.001 0.0015 0.002 0.0025 Distance (cm) 0.50 days 1.00 days 3.00 days 9.00 days 15.00 days -8 -7 -6 -5 -4 -3 -2 -1 0 0 0.002 0.004 0.006 0.008 0.01 Distance (cm) 0.50 days 1.00 days 3.00 days 9.00 days 15.00 days -8 -7 -6 -5 -4 -3 -2 -1 0 0 0.0001 0.0002 0.0003 0.0004 0.0005 Distance (cm) 0.50 days 1.00 days 3.00 days 9.00 days 15.00 days -8 -7 -6 -5 -4 -3 -2 -1 0 0 0.0003 0.0006 0.0009 0.0012 0.0015 0.0018 Distance (cm) 0.50 days 1.00 days 3.00 days 9.00 days 15.00 days Figure 11 – Profiles of molalities of sorbed K (top left), Ca (top right), Cd (bottom left), and Zn (bottom right) at selected times for the example CATEXCH. its functional groups. The higher the pH, the more functional groups of the organic matter are deprotonated and thus the higher the cation exchange capacity. This behavior is represented by a multi-site cation exchange complex consisting of six sites, each having a different selectivity coefficient for the exchange of protons (see Appelo et al., 1998). Finally, chloride is present in the soil solutions, resulting in the formation of aqueous complexes with the heavy metals. The soil profile is assumed to contain five distinct layers with different soil hydraulic properties and cation exchange capacities. Table 4 gives thicknesses of the different horizons, parameters for the van Genuchten’s equations for the wate(van Genuchten, 1980), and the total cation exchange capacities. The higher exchange capacities of the Bh1 and Bh2 horizons reflect their enrichment with the immobilized organic matter. Flow is assumed to be steady at a constant flux of 0.05 m day (18.25 m yearcauses the soil profile to be unsaturated (water contents vary between 0.37 and 0.15 as a function of depth). Table 3 pH and solution concentrations used in the simulation (µmol l Solution Mg Cd 0-28 cm depth 8.5 401.9 120 780 0.8 2.5 28-50 cm depth 8.5 454.0 120 780 0.0 Applied water 3.5 127.5 120 780 0.0 Concentration of Na is adjusted to obtain the desired pH. Table 4 Soil hydraulic properties and cation exchange capacities of five soil layers (Seuntjens, 2000). Horizon thickness (cm) s (cm day Cation exchange capacity (eq/1000 cm³ soil) A Bh1 Bh2 Bh/C 0.065 0.035 0.042 0.044 0.039 0.476 0.416 0.472 0.455 0.464 0.016 0.015 0.016 0.028 0.023 1.94 3.21 1.52 2.01 2.99 311 860 1198 0.5 0.5 0.5 0.5 0.5 0.0183 0.0114 0.0664 0.0542 0.0116 Table 5Overview of aqueous equilibrium reactions and corresponding equilibrium constants (data from phreeqc.dat database, Parkhurst and Appelo, 1999). Nr Aqueous speciation reaction (1) (2) (3) (4) (5) O = OH + H + HO = NaOH + H + HO = KOH + H O = CaOH + H + HO = MgOH + H -14 -14.18 -14.46 -12.78 -11.44 Cd (6) (7) (8) (9) (10) (11) (12) (13) + HO = XOH + H + 2 HO = X(OH) + 2 H + 3 HO = X(OH) + 3 H + 4 HO = X(OH) + 4 H = XCl + 2 Cl = XCl + 3 Cl = XCl + 4 Cl = XCl -10.08 -20.35 -33.30 -47.35 1.98 2.60 2.40 -7.71 -17.12 -28.06 -39.70 1.60 1.80 1.70 1.38 -8.96 -16.90 -28.40 -41.20 0.43 0.45 0.5 0.2 31 -0.5 -0.4 -0.3 -0.2 -0.1 0 3 4 5 6 7 8 9 Distance (m) 0.30 years 0.50 years 0.70 years 1.00 years -0.5 -0.4 -0.3 -0.2 -0.1 0 0 0.2 0.4 0.6 0.8 1 1.2 Distance (m) 0.30 yearss 0.50 yearss 0.70 yearss 1.00 yearss -0.5 -0.4 -0.3 -0.2 -0.1 0 0 0.1 0.2 0.3 0.4 0.5 0.6 Distance (m) 0.30 years 0.50 years 0.70 years 1.00 years -0.5 -0.4 -0.3 -0.2 -0.1 0 0 0.001 0.002 0.003 0.004 Distance (m) 0.30 years 0.50 years 0.70 years 1.00 years Figure 14 – Profiles of pH (top left), Cd (top right), the fraction of deprotonated cation exchange sites (bottom left), and the fraction of cation exchange sites with Cd (bottom right) at selected times for the example MCATEXCH. Print Information Unselect: T-Level information Select: Print at Regular Time Interval Time Interval: 0.025 (days) Print Times: Number of Print times: 5 Button: “Next” Print Times Button: "Default" Button: "OK" Check: "Make GNUplot Templates" This allows easy visualization of time series and profile data for variables, which are defined in thesection below in this dialog window and also defined in later in the editor Additional output of the Solute Transport – HP1 Water Flow – Iteration Criteria Button: “Next” Water Flow – Soil Hydraulic Model Button: “Next” Water Flow – Soil Hydraulic Parameters Qs: 0.35 Ks: 10 (cm/d) Button: “Next” Water Flow – Boundary Conditions Upper Boundary Condition: Constant Pressure Head Lower Boundary Condition: Constant Pressure Head Solute Transport – General Information Stability Criteria: 0.25 (to limit the time step) Number of Solutes: 6 Button: “Next” Six Components: Total_O, To: Redox sensitive components should be entered with the secondary master species, i.e., with their valence state between brackets. The primary master species of a redox ement name without a valence state, is not recognized as a component to be transported. Therefore, the primary master species C can not be entered here; one has to enter either C(4) or C(-4). Also, S is not allowed; one has to enter either S(6) or S(-2). Note that the HYDRUS GUI will not check if a correct master species is entered. Since the redox potential is high in this example (a high partial pressure of oxygen), the secondary master species Define the additional output to be written to selected output files. Button: "OK" Solute Transport – Solute Transport Parameters Bulk D : 1.8 (g/cm³) Disp: 1 (cm) Button: “Next” Upper Boundary Condition Bound. Cond. 3001 Soil Profile – Graphical Editor Button: "Edit Condition" Select All Top Value: 0 �: Conditions - Observation Points Button: "Insert" Insert 5 observation nodes, one for every 10 cm �: File - Save Data �: File – Exit Soil Profile – Summary Button: “Next” The standard HYDRUS-output can be viewed using commands in the right Post-processing part of the project window. Only the total concentrations of the components, which were defined in Solute Transport – HP1 Components dialog window can be viewed using the GUI H1D. HP1 creates a number of additional output files in the project folder. The path to the project �File - Project Manager Directory: gives the path A series of ASCII files containing command line instructions to generate time series () or profile () plots with the amount of the minerals gypsum and A series of ASCII files containing command line instructions to generate time series () or profile () plots with the change in the amount of the minerals gypsum and calcite using GNUPLOT; To view these various plots, the GNUPLOT code needs to be installed on your computer. GNUPLOT is freeware software that can be downloaded from that GNUPLOT (the wgnuplot.exe program for the Windows OS) is usually, after being After opening the Window version of GNUPLOxe, a plot can be directly generated by carrying out these commands: �File - Open Browse to project folder Open the template file of interest (*.plt) The figure can be adapted using line commands (see tutorials for GNUPLOT on the internet). The default terminal for the plots is Windows. We illustrate here only how a plot can be transferred to another terminal: Set terminal emf Set output ".emf" Replot Set terminal window Replot .emf file is created in the project folder. Overview of Selected Results: Time Series 5.5 6 6.5 7 7.5 8 8.5 9 9.5 0 0.5 1 1.5 2 2.5 -10.0 cm -20.0 cm -30.0 cm -40.0 cm -50.0 cm 1e-005 2e-005 3e-005 4e-005 5e-005 6e-005 0 0.5 1 1.5 2 2.5 Total concentration of C (mol/kg water) -20.0 cm -30.0 cm -40.0 cm -50.0 cm 0 0.004 0.008 0.012 0.016 0 0.5 1 1.5 2 2.5 Total concentration of Ca (mol/kg water) -20.0 cm -30.0 cm -40.0 cm -50.0 cm 0 0.004 0.008 0.012 0.016 0 0.5 1 1.5 2 2.5 Total concentration of S (mol/kg water) -20.0 cm -30.0 cm -40.0 cm -50.0 cm 0 1e-005 2e-005 3e-005 4e-005 0 0.5 1 1.5 2 2.5 gypsum (mol/1000 cm³ of soil) -20.0 cm -30.0 cm -40.0 cm -50.0 cm 0 1e-005 2e-005 3e-005 4e-005 5e-005 0 0.5 1 1.5 2 2.5 calcite (mol/1000 cm³ of soil) -20.0 cm -30.0 cm -40.0 cm -50.0 cm Figure 16 – Time series of pH (top left), total aqueous C concentration (top right), total aqueous Ca concentration (middle left), total aqueous S con the amount of gypsum (bottom left), and the amount of calcite (bottom right) at selected depths (observation nodes) during dissolution of calcite and gypsum. Button: "OK" Add the mineral otavite to theassemblage and define its initial amount Button: "OK" Add Cd to the list ofAdd otavite to the list ofto calculate the percentage of Cd in solution: then perCd = 100 * ("Cd") Note on headings: A specific format of the headings can be used to have an appropriate labeling of the axes in the GNUPLOT templates. The underscore _ is interpreted as a white space; the symbol @ separates the name of a variable from its unit. Thus, for the headings defined above, the corresponding axis text in the GNUPLOT template is "Per Button: "OK" Dissolution of gypsum and calcite and transport of Cd – the effect of higher Cl concentrations on the Cd mobility Aqueous components, which form strong complexes with Cd, will enhance the mobility of Cd. The same physical and geochemical set up as in the previous example (paragraph 4.2) is used here, but the composition of the inflowing water is changed after 1 day to a solution with a Project Manager Select project: "HP1-2" New Name: "HP1-3" Description: "Mineral dissolution/precipi Heading: Mineral dissolution/precipita Button: "OK" Time Information Check: "Time-Variable Boundary Conditions" Number of Time-Variable Boundary Conditions: 2 Button: "OK" Definitions of Solution Compositions Add solution 3002: The boundary Add solution 4001: The bottom Button: "OK" Button: "OK" Time Variable Boundary Conditions infiltration front (see Figure 18). Due to the high Cl concentrations, solubility of Cd is increased and otavite is not formed anymore after 1.5 days. 0 0.002 0.004 0.006 0.008 0.01 0.012 0.014 0.016 0.018 0.02 0 0.5 1 1.5 2 2.5 Total concentration of Cl (mol/kg water) -20.0 cm -30.0 cm -40.0 cm -50.0 cm Figure 19 – Time series of Cl at selected depths (observation nodes) for the example described in section 4.3. “Next” Print Information Number of Print Times: 12 "Select Print Times" “Next” Print Times Button: “Default” Button: “OK” Water Flow - Iteration Criteria Lower Time Step Multiplication Factor: 1 “Next” Water Flow - Soil Hydraulic Model “Next” Water Flow - Soil Hydraulic Parameters Catalog of Soil Hydraulic Properties: Loam Qs: 1 (Note: to have the same conditions as in the original comparable PHREEQC calculations) Ks: 0.00027777 (cm/s) “Next” Water Flow - Boundary Conditions “Next” Solute Transport - General Information Number of Solutes: 7 “Next” Add seven components: Total_O, Check: "Create PHREEQC.IN file using HYDRUS GUI" Button: “Next” Definitions of Solution CompositionsK-Na-N(5) solution Adapt the concentration of O(0) to be in equilibrium with the atmospheric “Next” Soil Profile - Graphical Editor Conditions�-Profile Discretization Number (from sidebar): 41 "Edit condition", select with the entire profile and specify 0 cm pressure "Insert", Insert a node at the bottom File-�Save Data File-�Exit Soil Profile - Summary “Next” : This exercise will produce the following warnings: "Master species N(3) is present in solution but is not transported.". The same warning occurs for N(0). N(3) and N(0) are two secondary master species from the primary master species N. Only the secondary master species N(5) was defined as a component to be transported (the Solute Transport – HP1 Components dialog window). HP1, however, checks if all components, which are present during the geochemical calculations, are defined in the transport model. If not, a warning message is generated. In our example, the concentrations of the components N(0) and N(3) are very low under the prevailing oxidizing conditions. Therefore, they can be neglected in the transport problem. If you want to avoid these warnings, you have to either include N(0) and N(3) as components to be transported or define an alternative primary master specDisplay results for “Observation Points” or “Profile Information”. Alternatively, Figure 20 can be created using information in the output file This example is the same as the one described in paragraph 4.5, except that time variable concentrations are appProject Manager New Name: CEC-2 Description: Transport and Cation Exchange, multiple pulses Heading: Transport and Cation Exchange, multiple pulses Time Information Time Units: hours Final Time: 60 (hr) Initial Time Step: 0.1 (hr) Minimum Time Step: 0.05 (hr) Maximum Time Step: 0.1 (hr) Number of Time-Variable Boundary Records: 4 “Next” Print Information Number of Print Times: 12 "Select Print Times" Default “Next” 60 3003 4001 Soil Profile - Graphical Editor "Insert", Insert nodes at 2, 4, 6, and 8 cm File-�Save Data File-�Exit Soil Profile - Summary “Next” Figure 21 gives the K concentration at different depths in the profile. Figure 22 shows the outflow concentration. The first pulse is identical to the single pulse project. Then additional solute pulses of different solution compositions will restart the cation exchange process depending on the incoming solution composition. 0 0.0002 0.0004 0.0006 0.0008 0.001 0.0012 0 10 20 30 40 50 60 Total concentration of K (mol/kg water)Time (hours) -2.0 cm -4.0 cm -6.0 cm -8.0 cm Figure 21 – Time series of K concentrations at four depths for the multiple-pulse cation exchange example. matter (proton dissociating groups on fulvic acids are 6 – 10 meq/g and 4 – 6 meq/g on humic Steady-state water flow of 1 cm day is assumed in this example. The composition of the inflowing water changes as a function of time: , Cl: 0.01 mol l mol l mol l28.9 – 80 days: Ca: 0.005 mol l, Cl: 0.01 mol lThese upper boundary conditions correspond with experimental conditions in a lysimeter experiment described in Seuntjens (2000). At the bottom of the lysimeter, capillary wicks with a length of 38 cm were installed. Taking into account the hydraulic properties of the wick and the steady-state water flow of 1 cm/d, the lower boundary pressure head is –28.3 cm. For the initial distribution of the pressure heads, it is assumed that the pressure head throughout the soil profile is initially in gravitational equilibrium with the lower boundary condition, (i.e. -28.3 at the bottom and -128.3 cm at the top, and lineaThe transport of 10 components is considered: Na, K, Ca, Mg, Cd, Zn, Pb, Cl, Br and C(4). In addition, Total_O and Total_H are included. Initial concentrations for the first nine components are given in Table 8. Br is used as a charge balance ion to have the desired initial pH, also defined in Table 8. O(0) and C(4) are considered in equilibrium with the atmospheric partial pressure of oxygen and carbon dioxide. Initial concentrations of Ca were Horizon Depth (cm) (g cm³) Organic Carbon s (cm Bh1 Bh2 C1 C2 0 – 7 19 – 24 24 – 28 28 – 50 50 – 75 75 – 100 1.31 1.59 1.3 1.38 1.41 1.52 1.56 2.75 0.75 4.92 3.77 0.89 0.12 0.08 0.065 0.035 0.042 0.044 0.039 0.030 0.021 0.48 0.42 0.47 0.46 0.46 0.42 0.39 0.016 0.015 0.016 0.028 0.023 0.021 0.021 1.94 3.21 1.52 2.01 2.99 2.99 2.99 95.04 311.04 38.88 864 1209.6 1209.6 1209.6 Table 8Initial pH and concentration for 9 components. (µmol/l) Button: "OK" Check: "Make GNUplot Templates" Water Flow – Iteration Criteria Button: “Next” Water Flow – Soil Hydraulic Model Button: “Next” Water Flow – Soil Hydraulic Parameters Insert the hydraulic properties from Table 7. Button: “Next” Water Flow – Boundary Conditions Upper Boundary Condition: Constant Flux Lower Boundary Condition: Constant Pressure Head Water Flow – Constant Boundary Fluxes Upper Boundary Flux: -1 (cm/day) (downward flux) Solute Transport – General Information Stability Criteria: 0.25 Number of Solutes: 12 Button: “Next” Twelve Components: Total_O, Total_H, Check: "Create PHREEQC.IN file using HYDRUS GUI" Button: “Next” Definitions of Solution CompositionsDefine the initial solutions for each of the seven layers (Table 8), and use solution numbers 1001-1007 and the keyword Adapt the concentration of O(0) and C(4) to be in equilibrium with the atmospheric partial pressure of : columns of , as well as the headings and the subheadings must be tab-delimited (see PHREEQC-2 manual, Parkhurst and to prepare the input for the keyword is to use MS Excel to make different input rows and columns and to copy it to the H1D GUI: Define the boundary condition 3001: Ca-Cl solution: low concentration Adapt the concentration of O(0) to be in equilibrium with the atmospheric Define the boundary condition 3002: Adapt the concentration of O(0) to be in equilibrium with the atmospheric Define the boundary condition 4001: Button: "OK" The geochemical model will be defined after different layers of the soil profile have been defined using Soil Profile – Graphical Editor. Information about the distribution of different layers can then be used in the definition of the geochemical Define the additional output to be written to selected output files. Button: "OK" Solute Transport – Solute Transport Parameters): 1.31, 1.59, 1.3, 1.38, 1.41, 1.52, 1.56 (g/cm³) Disp: 1 (cm) Button: “Next” Lower Boundary Condition: Ze Time series of Cl, Ca, and Cd at selected depths are shown in Figure 23. Cd concentration increases when Cl concentration increases due to aqueous complexation between Cd Horizontal Infiltration of MultipThis exercise simulates horizontal infiltration of multiple cations (Ca, Na, and K) into the initially dry soil column. It is vaguely based on experimental data presented by Smiles and Smith [2004]. The cation exchange between particular cations is descequation [White and Zelazny, 1986]. For an exchange reaction on an exchange site X involving N (2) (3) where [] denotes activity. The activity of the exchange species is equal to its equivalent fraction. The Gapon selectivity coefficients for Ca/Na, Ca/K, and Ca/Mg exchange are = 2.9, = 0.2, and GCaMg = 1.2. It is assumed that the cation exchange capacity (mol soil) Consider a soil column 20-cm long with an initial water content of 0.075. Infiltration occurs on the left side of the column under a constant water content equal to the saturated water content. Some physical parameters of the column are: bulk density = 1.75 g/cm³; dispersivity = 10 cm; the soil water retention characteristic and unsaturated hydraulic conductivity curve are described with the van Genuchten – Mualem model with the following parameters: = 0.307, = 0, = 246 cm/day, and = 0.5. The CEC is 55 meq/kg soil. As initial concentrations take: [Cl] = 1 mmol/kg water, [Ca] = 20 mmol/kg water, [K] = 2 mmol/kg water, [Na] = 5 mmol/kg water, [Mg] = 7.5 mmol/kg water, and [C(4)] = 1 mmol/kg water. The pH is 5.2, and the solution contains an unknown concentration of SO as a major ng composition: [Ca] = 0.002345 mol/kg water, [Na] = 0.01 mol/kg water, [K] = 0.0201 mol/kg water, [Mg] = 0, and [Cl] = 0.035 mol/kgw. The as major anion. Look at profile data of the water content, pH, concentrations of the cations and anions, and the amount of sorbed cations. Express sorbed concentration in meq/kg soil. The CEC should be expressed in mol/1000 cm of soil in HP1. Recalculate the amount of Answer: log KGK = 1.16 log KGCa = 0.462 log KGMg = 0.383] 4.7.3 Input Project Manager "New" Name: CEC-4 Description: Horizontal infiltration with Cation Exchange Heading: Horizontal infiltCheck "Water Flow" Check "Solute Transport" Select “HP1 (PHREEQC)” “Next” Depth of the soil profile: 20 (cm) “Next” Time Information Time Units: Minutes Final Time: 144 (min) Initial Time Step: 0.01 (min) Minimum Time Step: 0.01 (min) Maximum Time Step: 2 “Next” Print Information Number of Print Times: 6 Button "Select Print Times" Button “Next” Select: Make GNUPLOT templates Water Flow - Iteration Criteria Lower Time Step Multiplication Factor: 1.3 Button “Next” Water Flow - Soil Hydraulic Model Button “Next” Water Flow - Soil Hydraulic Parameters Equilibrate the exchange sites with the initial solution to ask for output of total concentrations of the components to save the absorbed concentrations as meq/kg soil. The default output in HP1 for an exchange species is mol/kg water. This can be NaG in or as a BASIC statement (10 ("NaG")) in . BASIC statements to convert 'mol/kg water' to 'meq/kg soil' can be added to following two variables are needed:The bulk density: use the HP1-specific BASIC statement ), where is the cell number of a given node, to obtain the bulk density for a given node. The number of the cell is obtained by the BASIC statement tot("water").Add meaningful headings for the punch output. 70 -20 -15 -10 -5 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 Distance (cm)Mass of water (kg/1000 cm³ of soil) 0 min 2.29 min 5.24 min 12.00 min 27.47 min 62.90 min 144.00 min -20 -15 -10 -5 0 0 0.005 0.01 0.015 0.02 0.025 0.03 0.035 Distance (cm)Total concentration of Cl (mol/kg water) 0 min 2.29 min 5.24 min 12.00 min 27.47 min 62.90 min 144.00 min -20 -15 -10 -5 0 0.0045 0.006 0.0075 0.009 Distance (cm) 2.29 min 5.24 min 12.00 min 27.47 min 62.90 min 144.00 min -20 -15 -10 -5 0 0.001 0.002 0.003 0.004 0.005 0.006 0.007 0.008 Distance (cm) 2.29 min 5.24 min 12.00 min 27.47 min 62.90 min 144.00 min -20 -15 -10 -5 0 0.008 0.01 0.012 0.014 0.016 0.018 0.02 0.022 Distance (cm)Total concentration of Ca (mol/kg water) 0 min 2.29 min 5.24 min 12.00 min 27.47 min 62.90 min 144.00 min -20 -15 -10 -5 0 0.003 0.004 0.005 0.006 0.007 0.008 Distance (cm)Total concentration of Mg (mol/kg water) 0 min 2.29 min 5.24 min 12.00 min 27.47 min 62.90 min 144.00 min Figure 24 – Profiles of water content (top left), and total aqueous concentrations of Cl, Na, K, Ca and Mg at selected print times during horizontal infiltration of multiple cations (the example is described in section 4.7). U Transport and Surface ComplexationThis exercise simulates the leaching of U under saturated, steady-state flow conditions. U adsorbs on Fe-oxides in the soil profile. Consider a 50-cm deep loamy soil with a saturated hydraulic conductivity of 1 cm/day. Take a porosity of 0.43, a bulk density of 1.31 g/cm³, and a dispersivity of 1 cm. The Fe content of the soil is 0.02 weight percentage. The capacity of the surface is calculated assuming that Fehas 0.875 reactive sites per mole of Fe (Waite et al., 1994). Following elements are considered: Ca, Cl, K, Mg, Na, U(6), and C(4). In this geochemical transport problem that is pH-sensitive, also Total_O and Total_H need to be transported. U adsorption is described by a non-electrostatic surface complexation model. As a consequence of this, a charge on the solid surface is not balanced by counter-ions in a double layer near the surface. Therefore, the aqueous phase will have a charge imbalance that will be of the same size, but having an opposite sign, as the charge on the surface. The entire system (i.e., solid surface + aqueous phase) will then be charged balanced. Therefore, also the 'Charge' of the aqueous solution has to be transported. Note that when an electrostatic surface complexation model, which takes into account the composition of the double layer, is used, the aqueous phase will be charged balanced, and so will be the solid surface and the double layer. A solution composition of rain water is assumed ry conditions: [Cl] = 69 µmol/kg water, [Ca] = 6 µmol/kg water, [K] = 4 µmol/kg water, [Na] = 64 µmol/kg water, ol/kg water, [Na] = 64 µmol/kg water, The concentration of O2 and CO2 are assumed to be in equilibrium with the atmospheric partial pressure of O2(g) and CO2(g). The U concentration in the initial solution composition is considered to be very low ([U] = 10-24 M), and much larger (10M) in the This problem is carried out using the PHREEQCU.DAT database. This is the PHREEQC.DAT database with the definition of additional U-species (from Langmuir, 1997 – a database from www.geo.tu-freiberg.de/~merkel/Wat4f_U.dat). Sorption is described reactions on the surface site called Hfo_w (line 3448 in the database). Solution complexation species are defined further in the database. Note that only one U-species adsorbs (uranyl): Hfo_wOH + UO2+2 = Hfo_wOUO2+ + H+ log_k 2.8 The capacity of the surface should be expressed in mol/1000 cm³ of soil. The capacity is calculated as: (0.0002) [g Fe/g soil] * 1.31 [g soil/cm3] * (1/160) [mol Fe/g Fe] * 2 [mol Fe/mol ] * 0.875 [moles sites/mol Fe ] * 1000 [cm³/1000cm³] = 0.00286 mol/1000 cm³ Lower Boundary Condition: Constant Pressure Head Solute Transport – General Information Stability Criteria: 0.25 Number of Solutes: 11 Button: “Next” Database Pathway: Browse: phreeqcU.dat Eleven Components: Total_O, Total_H, Char Check: "Create PHREEQC.IN file using the HYDRUS GUI" Button: “Next” Definitions of Solution CompositionsPut C and O in equilibrium with the atmospheric partial pressure of Define the boundary condition 3001: Put C and O in equilibrium with the atmospheric partial pressure of Select All Top Value : 0 �: Conditions - Observation Points Button: "Insert" Insert 5 observation nodes: add observation nodes at 0.5, 2, 5, 15, 25 and 50 cm�: File - Save Data �: File – Exit Soil Profile – Summary Button: “Next” U-profiles at selected print times are shown in Figure 26. -50 -40 -30 -20 -10 0 0 1e-009 2e-009 3e-009 Distance (cm) 40.00 days 80.00 days 120.00 days 160.00 days 200.00 days Profiles of aqueous concentration of U for the example described in section 4.8. In this example, we will simulate the transport and degradation of PCE and its daughter products in a soil column. Degradation not only occurs as sequential reactions, but also partly as parallel degradation reactions (see Figure 28). Degradation coefficients, yield factors and distribution Saturated flow conditions in a 2.0 m long soil column are maintained for 150 days. The Physical properties of the soil are a porosity of 0.5, the saturated hydraulic conductivity of 1 cm/day, and a dispersivity of 10 cm. Other soil hydraulic parameters are irrelevant for saturated Table 9 Definition of parameters and their values for the PCE biodegradation problem (from Case 1 and 2 in Sun et al., 2004). Rate parameters are for a reference temperature of 20°C. Parameter Symbol Verification Dispersion coefficient First-order degradation rate 1 Distribution factor, TCE to cis Distribution factor, TCE to trans Distribution factor, TCE to 1,1-DCE Yield coefficient, PCE to TCE Yield coefficient, VC to ETH v 1 2 3 4 5 6 7 1 2 3 1 2 3 4 m d-1 m² d-1 PCETCE 11 k22 1,1-DCE VCETH , k7 – Degradation pathway of PCE using first-order rate constants. Upper Boundary Condition: Constant Pressure Head Lower Boundary Condition: Free drainage Solute Transport – General Information Stability Criteria: 0.25 Number of Solutes: 9 Button: “Next” Six Components: Total_O, Total_H, Pce, Check: "Create PHREEQC.IN file using HYDRUS GUI" Button: “Next” Define new solution master species Define new solution species Define Rate equations Button: "OK" Define for each node the geochemical model, i.e., KINETIC keywords: Tce 1.0 Dcecis -0.5328 Dcetrans -0.111 Dceee - Button: "OK" Define the additional output to be written to selected output files. Button: "OK" Solute Transport – Solute Transport Parameters Bulk density: 1.5 (g/cm³) Disp: 10 (cm) Button: “Next” Upper Boundary Condition Bound. Cond. 3001 84 -200 -150 -100 -50 0 0 0.0005 0.001 0.0015 0.002 0.002 5 Distance (cm) 30.00 days 60.00 days 90.00 days 120.00 days 150.00 days -200 -150 -100 -50 0 0 0.0002 0.0004 0.0006 0.000 8 Distance (cm) 30.00 days 60.00 days 90.00 days 120.00 days 150.00 days Figure 30 – Profiles of Tce (left) and Eth (righ ) at selected print times for the example described in paragraph 4.9. 0 0.0002 0.0004 0.0006 0.0008 0.001 0.0012 0 20 40 60 80 100 120 140 160 Concentration (mol/kg water)Time (day) TCE PCE cis-DCE trans-DCE 1,1-DCE VC Eth Outflow curves for the example described in section 4.9. New Name: "TCE-2" Description: " TCE first-order degradtial value problem" Heading: TCE first-order degradation network: initial value problem Definitions of Solution Compositions Define an initial solution 1002 in equilibrium with the PCE_lq phase Define a pure water boundary solution Button: "OK" Button: "OK" Button: "OK" 88 0 0.0001 0.0002 0.0003 0.0004 0.0005 0.0006 0.0007 0 20 40 60 80 100 120 140 160 Concentration (mol/kg water)Time (day) TCE PCE cis-DCE trans-DCE 1,1-DCE VC Eth Outflow concentrations for the example described in section 4.10. Add the PCE contamination in the top 50 cm in the immobile zone. Numbers for the immobile zone starts at numbers of node +1 and end at two times the number of nodes. For this project, numbers for the immobile zone are thus from 102 to 202. PCE_lq 0 0.01 Button: "OK" ThImob: 0.1 Soil Profile – Graphical Editor Concentration number: 1 Button: "Edit Condition" Select all Solution composition: 1001 Concentration number: 1 Button: "Edit Condition" Select nodes 1-26 Solution composition: 2001 Button: "Edit Condition" Select nodes 27-101 Solution composition: 1001 �: File - Save Data �: File – Exit Coupled Nta Degradation and Biomass Growth The exercise is based on example 15 from the PHREEQC-2 manual (Parkhurst and Appel, 1999) and on the paper of Tebes-Stevens et al. (1998). The main topic is the biodegradation of nitrylotriacetate (Nta). of oxygen and biomass, is written as: (15)A multiplicative Monod rate expression is used to describe the Nta degradation: (16) is the rate of degradation [mol/l/hr], is the maximum specific rate (1.418E-3 mol/g cells/hr), is the biomass (initially 1.36E-4 g cells per liter of water), is the half saturation constant for substrate (7.64E-7 mol/l) and is the half saturation constant for acceptor (6.25e-6mol/l). The biomass production is described as: HNTa-2 (17) is the rate of cell growth [g cells/L/hr], is the microbial yield coefficient (65.14 g cells/mol Nta), and is the first-order biomass decay coefficient (0.00208 hrThe two equations (16) and (17) are coupled: Eq. (16) needs the current amount of biomass, Nta. PHREEQC Basic statements to be used in Consider a column of 5 m. The porosity is 0.4. A 0.2 m/hr is applied under saturated steady-state flow conditions. The dispersivity is 5 cm and the bulk density is 1.5 g/cm³. The Nta concentration in the infiltrating water is 5.23 µmol/kgw. Both the water contain 0.49 µmol/kgw C, 31.25 µmol/kgw O, 1000 µmol/kgw Na, and 1000 µmol/kgw Cl. Initially, there is 50 µg biomass per 1000 cm³ of soil. All other parameters are as defined Investigate time series and profile data of Nta and Biomass for an infiltration experiment of 24 Water Flow – Boundary Conditions Upper Boundary Condition: Constant Pressure Head Lower Boundary Condition: Constant Pressure Head Solute Transport – General Information Stability Criteria: 0.25 Number of Solutes: 7 Button: “Next” Database Pathway: Browse: ex15.dat Six Components: Total_O, To Check: "Create PHREEQC.IN file using HYDRUS GUI" Button: “Next” Define rate equations Definitions of Solution CompositionsDefine the boundary condition 3001: Button: "Edit Condition" Select All Top Value: 0 �: Conditions - Observation Points Button: "Insert" Insert 5 observation nodes at a depth interval of 1 m �: File - Save Data �: File – Exit Soil Profile – Summary Button: “Next” Time series and profiles of 0 1e-006 2e-006 3e-006 4e-006 5e-006 0 5 10 15 20 25 Total concentration of Nta (mol/kg water) -2.0 m -3.0 m -4.0 m -5.0 m 0 5e-005 0.0001 0.00015 0.0002 0.00025 0 5 10 15 20 25 biomass (mol/1000 cm³ of soil) -2.0 m -3.0 m -4.0 m -5.0 m Figure 36 – Time series of Nta concentrations and biomass at selected depths (observation nodes) for the example described in section 4.12. 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